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We can use

color yellow, resi 3
color yellow, resi 3-8

to colour one residue or a range of residues. But what if I want to colour residue 3-8 and 10-20, how to write it?

Also, my protein has two chains, light chain (L) with 100 residues and heavy chain (H) with 100 residues. How to colour the residue 10-20, 30-40 of light chain, and the residue 5-10, 20-30 of heavy chain in one go?

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  • $\begingroup$ What you’ve written isn’t valid Python code. Is this in Pymol or similar? $\endgroup$
    – Konrad Rudolph
    Commented Nov 15, 2017 at 18:21
  • $\begingroup$ @KonradRudolph it is Pymol code (you can use python with pymol but in the GUI you can type pymol code) $\endgroup$
    – Mitra
    Commented Nov 15, 2017 at 18:28
  • $\begingroup$ I don't think that python is an appropriate tag for this post. This really isn't a bioinformatics question. $\endgroup$
    – Bioathlete
    Commented Nov 15, 2017 at 23:57
  • $\begingroup$ there is no tag called "pymol", and where else would you recommend? $\endgroup$
    – lanselibai
    Commented Nov 16, 2017 at 10:01
  • 2
    $\begingroup$ of course each software may have its own mailing list, like I use Gromacs as well. But we should still be able to ask questions here @Mitra thank you for changing it to tag pymol. I thought I do not have the authority as a newbie. $\endgroup$
    – lanselibai
    Commented Nov 16, 2017 at 18:28

1 Answer 1

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Note: as I don't have any working version of pymol at the moment, I am not able to test the solution properly.
However, an easy way is to first create a selection, and then to color it:

select toBecolored, resi 3-8
color yellow, toBecolored

Regarding the L/H chain part, if they are effectively annotated as L and H, something like the following should work:

select toBeColored, ((i. 10-20 or i. 30-40) and c. L ) or ((i. 5-10+20-30) and c. H)
color yellow, toBeColored

Combining both commands is probably possible as:

color yellow, ((i. 10-20 or i. 30-40) and c. L ) or ((i. 5-10+20-30) and c. H)

Pymol allows synonyms (eg. resi and i. or chain and c.).

The following pages may be also helpful:

And the two following links, if you want to get a bit deeper in proper programming with python for pymol (as they can provide you with inspiration):

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    $\begingroup$ @Llopis: Thank you for the edit! It's a lot clearer now :) $\endgroup$
    – Mitra
    Commented Nov 16, 2017 at 14:54

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